M1 The three RNA polymerases characterization

and function M2 RNA Pol genes the ribisomal repeatⅠ M3 RNA Pol genes 5S and tRNA transcriptionⅢ M4 RNA Pol genes promoters and enhancersⅡ M5 General transcription factors and RNA Pol Ⅱ initiation

Section MmdashTranscription in eukaryotes

Molecular Biology

Transcription and its control are much more complex in eukaryotes

There are 3 RNA polymerases each specific for a subset of RNAs

M1 The three RNA polymerases characterization and function

Molecular Biology

Eukaryotic RNA polymerasesThe mechanism of eukaryotic transcription is similar to that in prokaryotes However the large number of polypeptides associated with the eukaryotic transcription machinery makes it far more complex Three different RNA polymerase complexes are responsible for the transcription of different types of eukaryotic genes The different RNA polymerases were identified by chromatographic purification of the enzymes and elution at different salt concentrations(Topic B4) Each RNA polymerase has a different sensitivity to the fungal toxin α-amanitin and this can be used to distinguish their activities

RNA polynerase (RNA pol ) transcribes most rRNA genes It is located in Ⅰ Ⅰthe nucleoli and is insensitive to α-amanitin

RNA polynerase (RNA pol ) transcribes all protein-coding genes and somⅡ Ⅱe small nuclear RNA(snRNA) genes It is located in the nucleoplasm and is very sensitive to α-amanitin

RNA polynerase (RNA pol ) transcribes the genes for tRNA 5S rRNA U6 Ⅲ Ⅲ snRNA and certain other small RNAs It is located in the nucleoplasm and is moderately sensitive to α-amanitin

In addition to these nuclear enzymes eukaryotic cells contain additional polymerase in mitochondria and chloroplasts

Molecular Biology

mRNA

rRNA

tRNA

snRNA

scRNA

7S RNA

micro RNA

There Are Many Functional Classes of RNA

Molecular Biology

ndash 500-700kDa 12+ subunits most of RNA pol II structures are determined The genes encoding the two largest subunits of each RNA polymerase have homology to each other 1048766bull The largest subunits of each eukaryotic RNA polymerase is similar to the βrsquo subunit of the E coli polymerase and the second largest subunit is similar to the βsubunit which contains the actiove site of the E coli enzyme

bull Two subunits which are common to RNA Pol I and RNA PolIII and a further subunit which is specific to RNA Pol II have homology to the E coli RNA polymerase αsubunit

bull At least five other smaller subunits are common to the three different polymerases Each polymerase also contains an additional four to seven subunits which are only present in one type

RNA polymerase subunits

Molecular Biology

Similar Structures of Bacterial (left) and Eukaryotic (right) RNA Polymerases

Molecular Biology

Like bacterial RNA polymerases each of the eukaryotic enzymes catalyzes transcription in a 5rsquo to 3rsquo direction and synthesizes RNA complementary to the antisense template strand

bullThe reaction requires the precursor nuckeotides ATP GTP CTP and UTP and does not requires a primer for transcription initiation

bullThe purified eukaryotic RNA polymerases unlike the purified bacterial enzymes require the presence of additional initiation proteins before they are able to bind to promoters and initiate transcription

Eukaryotic RNA polymerase activities

Molecular Biology

The CTD of RNA Pol II

CTD---C-terminal domain RNA Pol II RPB1 subunit has (CTD) with repeat (YSPTSPS)n n=26-52

In vitro studies have shown that the CTD sequence may be phosphorylated at the serines and tyrosines

Phosphorylate Unphosphorylated

Unphosphorylated to initiate transcription Phosphorylated for elongation

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

Transcription and its control are much more complex in eukaryotes

There are 3 RNA polymerases each specific for a subset of RNAs

M1 The three RNA polymerases characterization and function

Molecular Biology

Eukaryotic RNA polymerasesThe mechanism of eukaryotic transcription is similar to that in prokaryotes However the large number of polypeptides associated with the eukaryotic transcription machinery makes it far more complex Three different RNA polymerase complexes are responsible for the transcription of different types of eukaryotic genes The different RNA polymerases were identified by chromatographic purification of the enzymes and elution at different salt concentrations(Topic B4) Each RNA polymerase has a different sensitivity to the fungal toxin α-amanitin and this can be used to distinguish their activities

RNA polynerase (RNA pol ) transcribes most rRNA genes It is located in Ⅰ Ⅰthe nucleoli and is insensitive to α-amanitin

RNA polynerase (RNA pol ) transcribes all protein-coding genes and somⅡ Ⅱe small nuclear RNA(snRNA) genes It is located in the nucleoplasm and is very sensitive to α-amanitin

RNA polynerase (RNA pol ) transcribes the genes for tRNA 5S rRNA U6 Ⅲ Ⅲ snRNA and certain other small RNAs It is located in the nucleoplasm and is moderately sensitive to α-amanitin

In addition to these nuclear enzymes eukaryotic cells contain additional polymerase in mitochondria and chloroplasts

Molecular Biology

mRNA

rRNA

tRNA

snRNA

scRNA

7S RNA

micro RNA

There Are Many Functional Classes of RNA

Molecular Biology

ndash 500-700kDa 12+ subunits most of RNA pol II structures are determined The genes encoding the two largest subunits of each RNA polymerase have homology to each other 1048766bull The largest subunits of each eukaryotic RNA polymerase is similar to the βrsquo subunit of the E coli polymerase and the second largest subunit is similar to the βsubunit which contains the actiove site of the E coli enzyme

bull Two subunits which are common to RNA Pol I and RNA PolIII and a further subunit which is specific to RNA Pol II have homology to the E coli RNA polymerase αsubunit

bull At least five other smaller subunits are common to the three different polymerases Each polymerase also contains an additional four to seven subunits which are only present in one type

RNA polymerase subunits

Molecular Biology

Similar Structures of Bacterial (left) and Eukaryotic (right) RNA Polymerases

Molecular Biology

Like bacterial RNA polymerases each of the eukaryotic enzymes catalyzes transcription in a 5rsquo to 3rsquo direction and synthesizes RNA complementary to the antisense template strand

bullThe reaction requires the precursor nuckeotides ATP GTP CTP and UTP and does not requires a primer for transcription initiation

bullThe purified eukaryotic RNA polymerases unlike the purified bacterial enzymes require the presence of additional initiation proteins before they are able to bind to promoters and initiate transcription

Eukaryotic RNA polymerase activities

Molecular Biology

The CTD of RNA Pol II

CTD---C-terminal domain RNA Pol II RPB1 subunit has (CTD) with repeat (YSPTSPS)n n=26-52

In vitro studies have shown that the CTD sequence may be phosphorylated at the serines and tyrosines

Phosphorylate Unphosphorylated

Unphosphorylated to initiate transcription Phosphorylated for elongation

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

Eukaryotic RNA polymerasesThe mechanism of eukaryotic transcription is similar to that in prokaryotes However the large number of polypeptides associated with the eukaryotic transcription machinery makes it far more complex Three different RNA polymerase complexes are responsible for the transcription of different types of eukaryotic genes The different RNA polymerases were identified by chromatographic purification of the enzymes and elution at different salt concentrations(Topic B4) Each RNA polymerase has a different sensitivity to the fungal toxin α-amanitin and this can be used to distinguish their activities

RNA polynerase (RNA pol ) transcribes most rRNA genes It is located in Ⅰ Ⅰthe nucleoli and is insensitive to α-amanitin

RNA polynerase (RNA pol ) transcribes all protein-coding genes and somⅡ Ⅱe small nuclear RNA(snRNA) genes It is located in the nucleoplasm and is very sensitive to α-amanitin

RNA polynerase (RNA pol ) transcribes the genes for tRNA 5S rRNA U6 Ⅲ Ⅲ snRNA and certain other small RNAs It is located in the nucleoplasm and is moderately sensitive to α-amanitin

In addition to these nuclear enzymes eukaryotic cells contain additional polymerase in mitochondria and chloroplasts

Molecular Biology

mRNA

rRNA

tRNA

snRNA

scRNA

7S RNA

micro RNA

There Are Many Functional Classes of RNA

Molecular Biology

ndash 500-700kDa 12+ subunits most of RNA pol II structures are determined The genes encoding the two largest subunits of each RNA polymerase have homology to each other 1048766bull The largest subunits of each eukaryotic RNA polymerase is similar to the βrsquo subunit of the E coli polymerase and the second largest subunit is similar to the βsubunit which contains the actiove site of the E coli enzyme

bull Two subunits which are common to RNA Pol I and RNA PolIII and a further subunit which is specific to RNA Pol II have homology to the E coli RNA polymerase αsubunit

bull At least five other smaller subunits are common to the three different polymerases Each polymerase also contains an additional four to seven subunits which are only present in one type

RNA polymerase subunits

Molecular Biology

Similar Structures of Bacterial (left) and Eukaryotic (right) RNA Polymerases

Molecular Biology

Like bacterial RNA polymerases each of the eukaryotic enzymes catalyzes transcription in a 5rsquo to 3rsquo direction and synthesizes RNA complementary to the antisense template strand

bullThe reaction requires the precursor nuckeotides ATP GTP CTP and UTP and does not requires a primer for transcription initiation

bullThe purified eukaryotic RNA polymerases unlike the purified bacterial enzymes require the presence of additional initiation proteins before they are able to bind to promoters and initiate transcription

Eukaryotic RNA polymerase activities

Molecular Biology

The CTD of RNA Pol II

CTD---C-terminal domain RNA Pol II RPB1 subunit has (CTD) with repeat (YSPTSPS)n n=26-52

In vitro studies have shown that the CTD sequence may be phosphorylated at the serines and tyrosines

Phosphorylate Unphosphorylated

Unphosphorylated to initiate transcription Phosphorylated for elongation

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

mRNA

rRNA

tRNA

snRNA

scRNA

7S RNA

micro RNA

There Are Many Functional Classes of RNA

Molecular Biology

ndash 500-700kDa 12+ subunits most of RNA pol II structures are determined The genes encoding the two largest subunits of each RNA polymerase have homology to each other 1048766bull The largest subunits of each eukaryotic RNA polymerase is similar to the βrsquo subunit of the E coli polymerase and the second largest subunit is similar to the βsubunit which contains the actiove site of the E coli enzyme

bull Two subunits which are common to RNA Pol I and RNA PolIII and a further subunit which is specific to RNA Pol II have homology to the E coli RNA polymerase αsubunit

bull At least five other smaller subunits are common to the three different polymerases Each polymerase also contains an additional four to seven subunits which are only present in one type

RNA polymerase subunits

Molecular Biology

Similar Structures of Bacterial (left) and Eukaryotic (right) RNA Polymerases

Molecular Biology

Like bacterial RNA polymerases each of the eukaryotic enzymes catalyzes transcription in a 5rsquo to 3rsquo direction and synthesizes RNA complementary to the antisense template strand

bullThe reaction requires the precursor nuckeotides ATP GTP CTP and UTP and does not requires a primer for transcription initiation

bullThe purified eukaryotic RNA polymerases unlike the purified bacterial enzymes require the presence of additional initiation proteins before they are able to bind to promoters and initiate transcription

Eukaryotic RNA polymerase activities

Molecular Biology

The CTD of RNA Pol II

CTD---C-terminal domain RNA Pol II RPB1 subunit has (CTD) with repeat (YSPTSPS)n n=26-52

In vitro studies have shown that the CTD sequence may be phosphorylated at the serines and tyrosines

Phosphorylate Unphosphorylated

Unphosphorylated to initiate transcription Phosphorylated for elongation

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

ndash 500-700kDa 12+ subunits most of RNA pol II structures are determined The genes encoding the two largest subunits of each RNA polymerase have homology to each other 1048766bull The largest subunits of each eukaryotic RNA polymerase is similar to the βrsquo subunit of the E coli polymerase and the second largest subunit is similar to the βsubunit which contains the actiove site of the E coli enzyme

bull Two subunits which are common to RNA Pol I and RNA PolIII and a further subunit which is specific to RNA Pol II have homology to the E coli RNA polymerase αsubunit

bull At least five other smaller subunits are common to the three different polymerases Each polymerase also contains an additional four to seven subunits which are only present in one type

RNA polymerase subunits

Molecular Biology

Similar Structures of Bacterial (left) and Eukaryotic (right) RNA Polymerases

Molecular Biology

Like bacterial RNA polymerases each of the eukaryotic enzymes catalyzes transcription in a 5rsquo to 3rsquo direction and synthesizes RNA complementary to the antisense template strand

bullThe reaction requires the precursor nuckeotides ATP GTP CTP and UTP and does not requires a primer for transcription initiation

bullThe purified eukaryotic RNA polymerases unlike the purified bacterial enzymes require the presence of additional initiation proteins before they are able to bind to promoters and initiate transcription

Eukaryotic RNA polymerase activities

Molecular Biology

The CTD of RNA Pol II

CTD---C-terminal domain RNA Pol II RPB1 subunit has (CTD) with repeat (YSPTSPS)n n=26-52

In vitro studies have shown that the CTD sequence may be phosphorylated at the serines and tyrosines

Phosphorylate Unphosphorylated

Unphosphorylated to initiate transcription Phosphorylated for elongation

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

Similar Structures of Bacterial (left) and Eukaryotic (right) RNA Polymerases

Molecular Biology

Like bacterial RNA polymerases each of the eukaryotic enzymes catalyzes transcription in a 5rsquo to 3rsquo direction and synthesizes RNA complementary to the antisense template strand

bullThe reaction requires the precursor nuckeotides ATP GTP CTP and UTP and does not requires a primer for transcription initiation

bullThe purified eukaryotic RNA polymerases unlike the purified bacterial enzymes require the presence of additional initiation proteins before they are able to bind to promoters and initiate transcription

Eukaryotic RNA polymerase activities

Molecular Biology

The CTD of RNA Pol II

CTD---C-terminal domain RNA Pol II RPB1 subunit has (CTD) with repeat (YSPTSPS)n n=26-52

In vitro studies have shown that the CTD sequence may be phosphorylated at the serines and tyrosines

Phosphorylate Unphosphorylated

Unphosphorylated to initiate transcription Phosphorylated for elongation

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

Like bacterial RNA polymerases each of the eukaryotic enzymes catalyzes transcription in a 5rsquo to 3rsquo direction and synthesizes RNA complementary to the antisense template strand

bullThe reaction requires the precursor nuckeotides ATP GTP CTP and UTP and does not requires a primer for transcription initiation

bullThe purified eukaryotic RNA polymerases unlike the purified bacterial enzymes require the presence of additional initiation proteins before they are able to bind to promoters and initiate transcription

Eukaryotic RNA polymerase activities

Molecular Biology

The CTD of RNA Pol II

CTD---C-terminal domain RNA Pol II RPB1 subunit has (CTD) with repeat (YSPTSPS)n n=26-52

In vitro studies have shown that the CTD sequence may be phosphorylated at the serines and tyrosines

Phosphorylate Unphosphorylated

Unphosphorylated to initiate transcription Phosphorylated for elongation

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

The CTD of RNA Pol II

CTD---C-terminal domain RNA Pol II RPB1 subunit has (CTD) with repeat (YSPTSPS)n n=26-52

In vitro studies have shown that the CTD sequence may be phosphorylated at the serines and tyrosines

Phosphorylate Unphosphorylated

Unphosphorylated to initiate transcription Phosphorylated for elongation

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

M2 RNA Pol genes the ribosomal repeatⅠ

RNA polymerase ( RNA pol ) is responsible for the continuous syⅠ Ⅰnthesis of rRNA during interphase Human cells contain five clusters of around 40 copie of rRNA gene situated on different chromosomes (see Fig1 and Topic D4) Each rRNA gene produces a 45S rRNA transcript which is about 13000 nt long(see the Topic D4) This transcript is cleaved to give one copy each of the 28S RNA (5000 nt) 18S(2000nt) and 58S (160 nt) rRNA (see Topic O1) The continuous transcription of multiple gene copies of the RNAs is essential for sufficient production of the processed rRNAs which are packaged into ribosomes

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

Promoter

Transcription

Cleavage(the light pink regionsare degraded)

45S transcript

18S 58S 28S

5 318S 58S 28S

18S 58S 28SrRNA rRNA rRNA

Ribosomal RNA transcription units

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

Role of the nucleolus

Each rRNA cluster is known as a nucleolar organizer region since the nucleolus contains large loops of DNA correspondind to the gene clusters After a cell emerges from mitosis rRNA synthesis restarts and tiny nucleoli appear at the chromosomal locations of the rRNA genes During active rRNA synthesis the pre-rRNA transcripts are packed along the rRNA genes and may be visualized in the electron microscope as lsquoChrismas tree structuresrsquo In these structures the RNA transcripts are densely packed along the DNA and stick out perpendicularly from the DNA Short transcripts can be seen at the start of the gene which get longer until the end of the transcription unit which is indicated by disappearance of the RNA transcripts

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

RNA Pol I promoters

Mammalian pre-rRNA gene promoters have a bipartite transcription control region(Fig2) The core element includes the transcription start site and encompasses bases -31 to +6 This sequence is essential for transcription An additional element of around 50-80 bp named the upstream control element(UCE) begins about 100 bp upstream from the start site (-100) The UCE is responsible for an increase in transcription of around 10- to 100-fold compared with that from the core element alone

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

UBF A specific DNA-binding proteincalled upstream binding factor binds to the UCESL1 An additional factor called selectivity factor 1 is essential for RNA Pol transcription SL1 binds tⅠo and stabilizes the UBF-DNA complex and interacts with free downstream part of the core elementTBP One of the subunits of SL1 called TATA-binding protein is required for initiation by all three eukaryotic RNA polymerases

TAFI s（ TBP-associated factors） as the other subunits of SL1 and required for RNA polyⅠtranscription called TAFⅠs

Upstream binding factor

Schematic model for rRNA transcription initiation

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

M3 RNA Pol Genes 5S and tRNA traⅢnscription

RNA polymerase (RNA poly ) is a coⅢ Ⅲmplex of at 16 defferent subunits Like RNA Pol it is located in the nucleoplasⅡm RNA polymerase synthesizes the pⅢrecursors of 5S rRNA the tRNAs and snRNA and cytosolic RNAs

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

tRNA gene transcription

Why are the highly conserved sequences within the tRNA also highly conserved promoter DNA sequences

A box 5rsquo-TGGCNNAGTGG-3rsquo B box 5rsquo-GGTTCGANNCC-3rsquo

TFIIIB and TFIIIC are required for tRNA gene transcription

bull TFIIIB allows RNA Poly to binⅢd and initiate transcription

bull TFIIIC is an assembly factor for the positioning of the initiation factor TF BⅢ

Initiation of transcription at a eukaryotic tRNA promoter

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

The promoters of the 5S rRNA genes contain C box and A box as internal control regions

5S rRNA transcription initiation needs an additional assembly factor TF

AⅢ relative to the tRNA transcription initiation TF A Ⅲ acts to bind to C box and stabilize the interaction between TF C Ⅲ and 5S rRNA

5S rRNA gene transcription

Initiation of transcription at a eukaryotic 5S rRNA promoter

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

Many RNA Pol III genes also rely on upstream sequences for the regulation of their transcription Some promoters such as the U6 small nuclear RNA (U6 snRNA ) and small RNA genes from the Epstein-Barr virus use only regulatory sequences upstream from their transcription start sites The coding region of the U6 snRNA has a characteristic A box However this sequence is not required for transcription The U6 snRNA upstream sequence contains sequence typical of RNA Pol II promoters including a TATA box at bases -30 to -23 these promoters also share several other upstream transcription factor binding sequences with many U RNA genes which are transcribed by RNA Pol II These observations suggest that common transcription factors can regulate both RNA Pol II and RNA Pol III genes

Alternative RNA Pol promoters and RⅢNA Pol terminationⅢ

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology

RNA Pol terminationⅢ

Termination of transcription by RNA Pol appⅢears only to require polymerase recognition of a simple nucleotide sequence consisting of dA residues whose termination efficiency is affected by surrounding sequence Thus the sequence 5rsquo-GCAAAAGC-3rsquo is an efficient termination signal in the Xenopus borealis somatic 5SrRNA gene

Molecular Biology